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Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method

Year 2019, Volume 14, Issue 1, 150 - 154, 31.05.2019
https://doi.org/10.29233/sdufeffd.544174

Abstract

In this study, molecular docking studies were applied to three azo dyes, 2-[(3,5-diamino-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (A), 2-[(3,5-dimethyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (B) and 2-[(5-amino-3-methyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (C), which synthesized in our previous studies, to investigate their potential antibacterial properties. Modelling was performed on SwissDock web server using EADock DSS algorithm. Docking simulations of ligands (A, B and C) were performed into the E. coli beta-ketoacyl-acyl carrier protein synthase III (KAS III) active site to determine the probable binding conformations and inhibitory effects. Docking results were also compared with triclosan used as a commercial antibacterial agent and it was found that compound B had the best antibacterial property.

References

  • J. Lee, S. Kim, J. Sim, D. Lee, H. H. Kim, J. S. Hwang, D. G. Lee, Z. Y. Park, and J. I. Kim, “A potent antibacterial activity of new short D-enantiomeric lipopeptide against multi drug resistant bacteria,” Biochim Biophys Acta Biomembr., 1861, 34-42, 2019.
  • S. Tahir, T. Mahmood, F. Dastgir, I. Haq, A. Waseem, and U. Rashid, “Design, synthesis and anti-bacterial studies of piperazine derivatives against drug resistant bacteria,” Eur J Med Chem., 166, 224-231, 2019.
  • M. Caniçaa, V. Manageiro, H. Abriouel, J. Moran-Giladd, and C.M.A.P. Franzg, “Antibiotic resistance in foodborne bacteria,” Trends Food Sci. Technol., 84, 41-44, 2019.
  • I.J. Schalk, “Siderophoreeantibiotic conjugates: exploiting iron uptake to deliver drugs into bacteria,” Clin. Microbiol. Infect., 24, 801-802, 2018.
  • F. R. Fields, S. W. Lee, and M. J. McConnell, “Using bacterial genomes and essential genes for the development of new antibiotics,” Biochem. Pharmacol., 134, 74–86, 2017.
  • Ç. Karabacak Atay, T. Tilki, and B. Dede, “Design and synthesis of novel ribofuranose nucleoside analogues as antiproliferative agents: A molecular docking and DFT study,” J. Mol. Liq., 269, 315–326, 2018.
  • P. Sledz, and A. Caflisch, “Protein structure-based drug design: from docking to molecular Dynamics,” Curr. Opin. Struc. Biol., 48, 93–102, 2018.
  • S. Kumar, and S. Kumar, “Chapter 6: Molecular Docking: A Structure-Based Approach for Drug Repurposing,” In Silico Drug Design, 161-189, 2019.
  • K. A. Ramsbottoma, D. F. Carrb, A. R. Jonesa, and D. J. Rigdena, “Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions,” Mol. Immunol., 101, 488-499, 2018.
  • Ç. Karabacak Atay, M. Gokalp, S. Ozdemir Kart, and T. Tilki, “Mono azo dyes derived from 5-nitroanthranilic acid: Synthesis, absorption properties and DFT calculations,” J. Mol. Struct., 1141, 237-244, 2017.
  • A. Grosdidier, V. Zoete, and O. Michielin, “SwissDock, a protein-small molecule docking web service based on EADock DSS,” Nucleic Acids Res., 39, 270-277, 2011.
  • Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., (2000). The Protein Data Bank. Nucleic Acids Res., 28(1), 235–242.
  • Gaussian 09, Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.
  • E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin, “UCSF Chimera--a visualization system for exploratory research and analysis,” J. Comput. Chem., 13, 1605-1612, 2004.
  • A.D. Becke, “Density-functional exchange-energy approximation with correct asymptotic behavior,” Phys. Rev. A, 38, 3098-3100, 1988.
  • C. Lee, W. Yang, and R.G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B, 37, 785-789, 1988.

Moleküler Docking Yöntemi ile Bazı Azo Bileşiklerinin Potansiyel Antibakteriyel Özelliklerinin İncelenmesi

Year 2019, Volume 14, Issue 1, 150 - 154, 31.05.2019
https://doi.org/10.29233/sdufeffd.544174

Abstract

Bu çalışmada, önceki çalışmalarımızda sentezlediğimiz  üç azo boyarmaddenin, 2 - [(3,5-diamino-1H-pirazol-4-il)diazenil]-5-nitrobenzoik asit (A), 2-[(3,5)-dimetil-1H-pirazol-4-il) diazenil]-5-nitrobenzoik asit (B) ve 2-[(5-amino-3-metil-1H-pirazol-4-il) diazenil]-5-nitrobenzoik asit (C), potansiyel antibakteriyel özelliklerini araştırmak için moleküler doking çalışmaları yapıldı. Modelleme, SwissDock web sunucusunda EADock DSS algoritması kullanılarak gerçekleştirildi. Olası bağlanma konformasyonları ve inhibe edici etkileri belirlemek için E. coli beta-ketoaçil-açil taşıyıcı protein sentaz III (KAS III) aktif bölgesine ligandların (A, B ve C) bağlanma simülasyonları yapıldı. Doking sonuçları ayrıca ticari bir antibakteriyel madde olarak kullanılan triklosan ile karşılaştırıldı ve B bileşiğinin en iyi antibakteriyel özelliğe sahip olduğu bulundu.

References

  • J. Lee, S. Kim, J. Sim, D. Lee, H. H. Kim, J. S. Hwang, D. G. Lee, Z. Y. Park, and J. I. Kim, “A potent antibacterial activity of new short D-enantiomeric lipopeptide against multi drug resistant bacteria,” Biochim Biophys Acta Biomembr., 1861, 34-42, 2019.
  • S. Tahir, T. Mahmood, F. Dastgir, I. Haq, A. Waseem, and U. Rashid, “Design, synthesis and anti-bacterial studies of piperazine derivatives against drug resistant bacteria,” Eur J Med Chem., 166, 224-231, 2019.
  • M. Caniçaa, V. Manageiro, H. Abriouel, J. Moran-Giladd, and C.M.A.P. Franzg, “Antibiotic resistance in foodborne bacteria,” Trends Food Sci. Technol., 84, 41-44, 2019.
  • I.J. Schalk, “Siderophoreeantibiotic conjugates: exploiting iron uptake to deliver drugs into bacteria,” Clin. Microbiol. Infect., 24, 801-802, 2018.
  • F. R. Fields, S. W. Lee, and M. J. McConnell, “Using bacterial genomes and essential genes for the development of new antibiotics,” Biochem. Pharmacol., 134, 74–86, 2017.
  • Ç. Karabacak Atay, T. Tilki, and B. Dede, “Design and synthesis of novel ribofuranose nucleoside analogues as antiproliferative agents: A molecular docking and DFT study,” J. Mol. Liq., 269, 315–326, 2018.
  • P. Sledz, and A. Caflisch, “Protein structure-based drug design: from docking to molecular Dynamics,” Curr. Opin. Struc. Biol., 48, 93–102, 2018.
  • S. Kumar, and S. Kumar, “Chapter 6: Molecular Docking: A Structure-Based Approach for Drug Repurposing,” In Silico Drug Design, 161-189, 2019.
  • K. A. Ramsbottoma, D. F. Carrb, A. R. Jonesa, and D. J. Rigdena, “Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions,” Mol. Immunol., 101, 488-499, 2018.
  • Ç. Karabacak Atay, M. Gokalp, S. Ozdemir Kart, and T. Tilki, “Mono azo dyes derived from 5-nitroanthranilic acid: Synthesis, absorption properties and DFT calculations,” J. Mol. Struct., 1141, 237-244, 2017.
  • A. Grosdidier, V. Zoete, and O. Michielin, “SwissDock, a protein-small molecule docking web service based on EADock DSS,” Nucleic Acids Res., 39, 270-277, 2011.
  • Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., (2000). The Protein Data Bank. Nucleic Acids Res., 28(1), 235–242.
  • Gaussian 09, Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.
  • E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin, “UCSF Chimera--a visualization system for exploratory research and analysis,” J. Comput. Chem., 13, 1605-1612, 2004.
  • A.D. Becke, “Density-functional exchange-energy approximation with correct asymptotic behavior,” Phys. Rev. A, 38, 3098-3100, 1988.
  • C. Lee, W. Yang, and R.G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B, 37, 785-789, 1988.

Details

Primary Language English
Subjects Engineering, Chemical
Journal Section Makaleler
Authors

Çiğdem KARABACAK ATAY
BURDUR MEHMET AKİF ERSOY ÜNİVERSİTESİ
0000-0001-7226-9971
Türkiye


Tahir TİLKİ (Primary Author)
SÜLEYMAN DEMİREL ÜNİVERSİTESİ
0000-0002-1040-2375
Türkiye


Bülent DEDE
SÜLEYMAN DEMİREL ÜNİVERSİTESİ
0000-0003-1416-7373
Türkiye

Publication Date May 31, 2019
Published in Issue Year 2019, Volume 14, Issue 1

Cite

Bibtex @research article { sdufeffd544174, journal = {Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi}, issn = {}, eissn = {1306-7575}, address = {}, publisher = {Süleyman Demirel University}, year = {2019}, volume = {14}, pages = {150 - 154}, doi = {10.29233/sdufeffd.544174}, title = {Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method}, key = {cite}, author = {Karabacak Atay, Çiğdem and Tilki, Tahir and Dede, Bülent} }
APA Karabacak Atay, Ç. , Tilki, T. & Dede, B. (2019). Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method . Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi , 14 (1) , 150-154 . DOI: 10.29233/sdufeffd.544174
MLA Karabacak Atay, Ç. , Tilki, T. , Dede, B. "Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method" . Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi 14 (2019 ): 150-154 <https://dergipark.org.tr/en/pub/sdufeffd/issue/45380/544174>
Chicago Karabacak Atay, Ç. , Tilki, T. , Dede, B. "Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method". Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi 14 (2019 ): 150-154
RIS TY - JOUR T1 - Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method AU - Çiğdem Karabacak Atay , Tahir Tilki , Bülent Dede Y1 - 2019 PY - 2019 N1 - doi: 10.29233/sdufeffd.544174 DO - 10.29233/sdufeffd.544174 T2 - Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi JF - Journal JO - JOR SP - 150 EP - 154 VL - 14 IS - 1 SN - -1306-7575 M3 - doi: 10.29233/sdufeffd.544174 UR - https://doi.org/10.29233/sdufeffd.544174 Y2 - 2019 ER -
EndNote %0 Süleyman Demirel University Faculty of Arts and Science Journal of Science Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method %A Çiğdem Karabacak Atay , Tahir Tilki , Bülent Dede %T Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method %D 2019 %J Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi %P -1306-7575 %V 14 %N 1 %R doi: 10.29233/sdufeffd.544174 %U 10.29233/sdufeffd.544174
ISNAD Karabacak Atay, Çiğdem , Tilki, Tahir , Dede, Bülent . "Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method". Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi 14 / 1 (May 2019): 150-154 . https://doi.org/10.29233/sdufeffd.544174
AMA Karabacak Atay Ç. , Tilki T. , Dede B. Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method. Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi. 2019; 14(1): 150-154.
Vancouver Karabacak Atay Ç. , Tilki T. , Dede B. Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method. Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi. 2019; 14(1): 150-154.
IEEE Ç. Karabacak Atay , T. Tilki and B. Dede , "Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method", Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi, vol. 14, no. 1, pp. 150-154, May. 2019, doi:10.29233/sdufeffd.544174